After the preliminary editing of the data file (4-20microarray_data.vcf.gz), columns REF and ALT were found to have values not compatible with VCF standard. The data file needs to be updated before we can process this submission.  

The data after preliminary processing is shown below:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
1       145770680       1_145770680_A_<DEL>     A       <DEL>   .       PASS    VRT=2;Samplename=Sample
1       146023923       1_146023923_C_<DEL>     C       <DEL>   .       PASS    VRT=2;Samplename=Sample
1       146043714       1_146043714_A_<DEL>     A       <DEL>   .       PASS    VRT=2;Samplename=Sample
1       168061817       1_168061817_G_<DEL>     G       <DEL>   .       PASS    VRT=2;Samplename=Sample
2       970389  2_970389_G_<DUP>        G       <DUP>   .       PASS    VRT=2;Samplename=Sample
2       158567199       2_158567199_C_<DEL>     C       <DEL>   .       PASS    VRT=2;Samplename=Sample
3       183265471       3_183265471_C_<DEL>     C       <DEL>   .       PASS    VRT=2;Samplename=Sample
4       68346   4_68346_T_<DEL> T       <DEL>   .       PASS    VRT=2;Samplename=Sample
4       68346   4_68346_T_<DEL> T       <DEL>   .       PASS    VRT=2;Samplename=Sample
4       27002834        4_27002834_G_<DEL>      G       <DEL>   .       PASS    VRT=2;Samplename=Sample
4       116796181       4_116796181_C_<DUP>     C       <DUP>   .       PASS    VRT=2;Samplename=Sample
5       129135230       5_129135230_T_<DEL>     T       <DEL>   .       PASS    VRT=2;Samplename=Sample
6       163579586       6_163579586_G_<DEL>     G       <DEL>   .       PASS    VRT=2;Samplename=Sample
6       166870453       6_166870453_G_<DEL>     G       <DEL>   .       PASS    VRT=2;Samplename=Sample
7       4905410 7_4905410_C_<DUP>       C       <DUP>   .       PASS    VRT=2;Samplename=Sample
7       72701099        7_72701099_T_<DEL>      T       <DEL>   .       PASS    VRT=2;Samplename=Sample
8       77868023        8_77868023_A_<DUP>      A       <DUP>   .       PASS    VRT=2;Samplename=Sample
10      13986172        10_13986172_G_<DUP>     G       <DUP>   .       PASS    VRT=2;Samplename=Sample
11      117507946       11_117507946_T_<DUP>    T       <DUP>   .       PASS    VRT=2;Samplename=Sample
12      173787  12_173787_C_<DUP>       C       <DUP>   .       PASS    VRT=2;Samplename=Sample
13      109549536       13_109549536_C_<DEL>    C       <DEL>   .       PASS    VRT=2;Samplename=Sample
14      72942932        14_72942932_T_<DUP>     T       <DUP>   .       PASS    VRT=2;Samplename=Sample
14      103384404       14_103384404_C_<DEL>    C       <DEL>   .       PASS    VRT=2;Samplename=Sample
15      23288350        15_23288350_C_<DUP>     C       <DUP>   .       PASS    VRT=2;Samplename=Sample
18      136227  18_136227_T_<DEL>       T       <DEL>   .       PASS    VRT=2;Samplename=Sample
18      136227  18_136227_T_<DUP>       T       <DUP>   .       PASS    VRT=2;Samplename=Sample
20      56992677        20_56992677_A_<DEL>     A       <DEL>   .       PASS    VRT=2;Samplename=Sample
22      16888900        22_16888900_G_<DUP>     G       <DUP>   .       PASS    VRT=2;Samplename=Sample
22      18916843        22_18916843_A_<DEL>     A       <DEL>   .       PASS    VRT=2;Samplename=Sample
22      20716877        22_20716877_G_<DEL>     G       <DEL>   .       PASS    VRT=2;Samplename=Sample
X       168547  X_168547_C_<DEL>        C       <DEL>   .       PASS    VRT=2;Samplename=Sample
X       372013  X_372013_C_<DEL>        C       <DEL>   .       PASS    VRT=2;Samplename=Sample
X       6455152 X_6455152_A_<DEL>       A       <DEL>   .       PASS    VRT=2;Samplename=Sample
X       6885116 X_6885116_G_<DEL>       G       <DEL>   .       PASS    VRT=2;Samplename=Sample
Y       2650425 Y_2650425_T_<DUP>       T       <DUP>   .       PASS    VRT=2;Samplename=Sample
Y       2780528 Y_2780528_A_<DUP>       A       <DUP>   .       PASS    VRT=2;Samplename=Sample